Thanks dac and jason for your replies.
I am using pmemd with amber14.
Regarding autoimage; in general cpptraj gives the following error:
Error: Could not determine trajectory merged.prmtop format.
trajectories are in binary format.
best
morteza
________________________________
From: Khabiri, Morteza
Sent: Thursday, October 15, 2015 2:46 PM
To: amber.ambermd.org
Subject: FW: System gets unwrap while iwrap=1 in ti
Dear Jason
I have replied you in the morning. It did not sent to amber list since it contain jpg file (I think).
I am doing MD in isotropic NVT ensemble. So, I dont have any slab geometry in my MD. The box size is qiute enough that the distance btw protein and the wall is bigger that the half of the box size.
Regarding unwrap: I would say I mean the solution(water + ions) diffused out of the box while the box size is kept fixed.
The same system as the one for ti calculations, was running before in NVT and iwrap=1 but in MD calculation and the wrap working well. All molecules kept in the simulation box and not diffuse out of the box. But, when I use the same syetem for ti calculation, the iwrap is not working anymore. Anyway, It should not effect the energy calculation but I am wondering why it is iwrap not working in ti calculation.
Please let me know if the description is not clear.
Thanks
Morteza
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Received on Fri Oct 16 2015 - 07:00:03 PDT
